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PDBsum entry 2o9p

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protein links
Hydrolase PDB id
2o9p
Jmol
Contents
Protein chain
445 a.a. *
Waters ×138
* Residue conservation analysis
PDB id:
2o9p
Name: Hydrolase
Title: Beta-glucosidase b from paenibacillus polymyxa
Structure: Beta-glucosidase b. Chain: a. Synonym: gentiobiase, cellobiase, beta-d- glucoside glucohydrolase, amygdalase. Engineered: yes
Source: Paenibacillus polymyxa. Organism_taxid: 1406. Gene: bglb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.235     R-free:   0.275
Authors: P.Isorna,J.Polaina,J.Sanz-Aparicio
Key ref:
P.Isorna et al. (2007). Crystal structures of Paenibacillus polymyxa beta-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. J Mol Biol, 371, 1204-1218. PubMed id: 17585934 DOI: 10.1016/j.jmb.2007.05.082
Date:
14-Dec-06     Release date:   02-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22505  (BGLB_PAEPO) -  Beta-glucosidase B
Seq:
Struc:
448 a.a.
445 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.21  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/j.jmb.2007.05.082 J Mol Biol 371:1204-1218 (2007)
PubMed id: 17585934  
 
 
Crystal structures of Paenibacillus polymyxa beta-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases.
P.Isorna, J.Polaina, L.Latorre-García, F.J.Cañada, B.González, J.Sanz-Aparicio.
 
  ABSTRACT  
 
Bacteria species involved in degradation of cellulosic substrates produce a variety of enzymes for processing related compounds along the hydrolytic pathway. Paenibacillus polymyxa encodes two homologous beta-glucosidases, BglA and BglB, presenting different quaternary structures and substrate specificities. We previously reported the 3D-structure of BglA, which is highly specific against cellobiose. Here, we present structural analysis of BglB, a monomeric enzyme that acts as an exo-beta-glucosidase hydrolyzing cellobiose and cellodextrins of higher degree of polymerization. The crystal structure of BglB shows that several polar residues narrow the active site pocket and contour additional subsites. The structure of the BglB-cellotetraose complex confirms these subsites, revealing the substrate-binding mode, and shows the oligosaccharide-enzyme recognition pattern in detail. Comparison between BglA and BglB crystal structures suggests that oligomerization in BglA can assist in fine-tuning the specificity of the active centre by modulating the loops surrounding the cavity. We have solved the crystal structure of BglB with bound thiocellobiose, a competitive inhibitor, which together with the BglB-cellotetraose complex delineate the general features of the aglycon site. The detailed characterization of the atomic interactions at the aglycon site show a recognition pattern common to all bacterial beta-glucosidases, and presents some differences with the aglycon site in plant beta-glycosidases essentially by means of a different orientation of the basal Trp. The crystal structures of of BglB with a covalently bound inhibitor (derived from 2-fluoroglucoside) and glucose (produced by hydrolysis of the substrate in the crystal), provide additional pictures of the binding events and the intermediates formed during the reaction. Altogether, this information can assist in the understanding of subtle differences of the enzyme mechanism and substrate recognition within this family of enzymes, and consequently it can help in the development of new enzymes with improved activity or specificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Scheme of the general glycosidase mechanism for retaining β-glycosidases, proceeding through a covalent intermediate.
Figure 4.
Figure 4. Bonding interactions of ligands in the active site of BglB. (a) 2-Deoxy-2-fluoro-α-d-glucosyl in the 2FGlc/BglB complex; (b) thiocellobiose in the Tcb/BglB complex; (c) glucose in the Glc/BglB complex; and (d) cellotetraose in the CTT/BglB complex. Only residues linked by hydrogen bond are shown in each case, and the catalytic glutamate residues are highlighted. Water molecules involved in ligand recognition are represented.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 1204-1218) copyright 2007.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20376631 C.S.Park, M.H.Yoo, K.H.Noh, and D.K.Oh (2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.
  Appl Microbiol Biotechnol, 87, 9.  
19955176 M.Behrendt, J.Polaina, and H.Y.Naim (2010).
Structural hierarchy of regulatory elements in the folding and transport of an intestinal multidomain protein.
  J Biol Chem, 285, 4143-4152.  
19415755 H.Nassif, H.Al-Ali, S.Khuri, and W.Keirouz (2009).
Prediction of protein-glucose binding sites using support vector machines.
  Proteins, 77, 121-132.  
18615662 A.D.Hill, and P.J.Reilly (2008).
Computational analysis of glycoside hydrolase family 1 specificities.
  Biopolymers, 89, 1021-1031.  
18712828 K.H.Nam, S.J.Kim, M.Y.Kim, J.H.Kim, Y.S.Yeo, C.M.Lee, H.K.Jun, and K.Y.Hwang (2008).
Crystal structure of engineered beta-glucosidase from a soil metagenome.
  Proteins, 73, 788-793.
PDB code: 3cmj
18378601 L.G.Ljungdahl (2008).
The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.
  Ann N Y Acad Sci, 1125, 308-321.  
18422657 L.M.Mendonça, and S.R.Marana (2008).
The role in the substrate specificity and catalysis of residues forming the substrate aglycone-binding site of a beta-glycosidase.
  FEBS J, 275, 2536-2547.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.